2MAD | Genus

Total Genus 29

The genus trace: a function that shows values of genus (vertical axis) for subchains spanned between the first residue, and all other residues (shown on horizontal axis). The number of the latter residue and the genus of a given subchain are shown interactively.

Total Genus	29
Knots found	KnotProt 2.0: K
sequence length	124
structure length	123
Chain Sequence	VDPRAKWQPQDNDIQACDYWRHCSIDGNICDCSGGSLTNCPPGTKLATASVASCYNPTDGQSYLIAYRDCCGYNVSGRCPCLNTEGELPVYRPEFANDIIWCFGAEDDAMTYHCTISPIVGKA

The genus matrix. At position (x,y) a genus value for a subchain spanned between x’th and y’th residue is shown. Values of the genus are represented by color, according to the scale given on the right.

Structure visualization

loadScript /static/js/j2s/core/package.js

loadScript /static/js/j2s/core/corejmol.z.js

loadScript /static/js/j2s/core/corescript.z.js

JSmol exec jmolApplet0 start applet null

Jmol JavaScript applet jmolApplet0__5400713084503215__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__5400713084503215__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://genus.fuw.edu.pl/view/2mad/L/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__5400713084503215__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"5400713084503215","bgcolor":"white" }

setting document base to "https://genus.fuw.edu.pl/view/2mad/L/"

Jmol Version: 14.29.13 2018-04-17 17:17

java.vendor: Java2Script (HTML5)

java.version: 2018-01-28 23:38:52 (JSmol/j2s)

os.name: Mozilla/5.0 AppleWebKit/537.36 (KHTML, like Gecko; compatible; ClaudeBot/1.0; +claudebot@anthropic.com)

Access: ALL

memory: 0.0/0.0

processors available: 1

useCommandThread: false

appletId:jmolApplet0 (signed)

Jmol getValue emulate null

defaults = "Jmol"

Jmol getValue boxbgcolor null

Jmol getValue bgcolor white

backgroundColor = "white"

Jmol getValue ANIMFRAMECallback null

Jmol getValue APPLETREADYCallback Jmol._readyCallback

APPLETREADYCallback = "Jmol._readyCallback"

callback set for APPLETREADYCallback Jmol._readyCallback APPLETREADY

Jmol getValue ATOMMOVEDCallback null

Jmol getValue AUDIOCallback null

Jmol getValue CLICKCallback null

Jmol getValue DRAGDROPCallback null

Jmol getValue ECHOCallback null

Jmol getValue ERRORCallback null

Jmol getValue EVALCallback null

Jmol getValue HOVERCallback null

Jmol getValue IMAGECallback null

Jmol getValue LOADSTRUCTCallback null

Jmol getValue MEASURECallback null

Jmol getValue MESSAGECallback null

Jmol getValue MINIMIZATIONCallback null

Jmol getValue SERVICECallback null

Jmol getValue PICKCallback null

Jmol getValue RESIZECallback null

Jmol getValue SCRIPTCallback null

Jmol getValue SYNCCallback null

Jmol getValue STRUCTUREMODIFIEDCallback null

Jmol getValue doTranslate null

language=en_US

Jmol getValue popupMenu null

Jmol getValue script null

Jmol getValue loadInline null

Jmol getValue load null

Jmol applet jmolApplet0__5400713084503215__ ready

script 1 started

platformSpeed = 8

Viewer cachePut cache://localLOAD_/file/5cfd514990fea93bf241b896/pdb.gz

Viewer cachePut https://genus.fuw.edu.pl/file/5cfd514990fea93bf241b896/pdb.gz

FileManager.getAtomSetCollectionFromFile(/file/5cfd514990fea93bf241b896/pdb.gz)

loadScript /static/js/j2s/core/corezip.z.js

The Resolver thinks Pdb

loadScript /static/js/j2s/core/corebio.z.js

Time for openFile(/file/5cfd514990fea93bf241b896/pdb.gz): 619 ms

reading 123 atoms

ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false

1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.

Default Van der Waals type for model set to Jmol

123 atoms created

ModelSet: autobonding; use autobond=false to not generate bonds automatically

Time for creating model: 23 ms

Adding embedded #jmolscript: select ({0:122});backbone only;select *;

platformSpeed = 8

cartoonsFancy = true

sheetSmoothing = 1.0

traceAlpha = true

loadScript /static/js/j2s/core/corescriptcmd.z.js

specularPower = 9

ambientPercent = 20

antialiasDisplay = true

Script completed

Jmol script terminated

loadScript /static/js/j2s/J/g3d/HermiteRenderer.js

loadScript /static/js/j2s/J/renderbio/BioMeshRenderer.js

loadScript /static/js/j2s/J/render/MeshRenderer.js

loadScript /static/js/j2s/J/shape/Mesh.js

After clicking on a point (x,y) in the genus matrix above, a subchain from x to y is shown in color.

Genus data interpretation

Chord Diagram

publication title	Active site structure of methylamine dehydrogenase: hydrazines identify C6 as the reactive site of the tryptophan-derived quinone cofactor. pubmed doi rcsb
molecule keywords	METHYLAMINE DEHYDROGENASE (LIGHT SUBUNIT)
molecule tags	Oxidoreductase(chnh2(d)-deaminating)
source organism	Paracoccus versutus
total genus	29
structure length	123
sequence length	124
other databases	KnotProt 2.0: K
ec nomenclature	ec 1.4.9.1: Methylamine dehydrogenase (amicyanin).
pdb deposition date	1992-05-20

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
L	PF02975	Me-amine-dh_L	Methylamine dehydrogenase, L chain

Image from the rcsb pdb (www.rcsb.org)

cath code	Class	Architecture	Topology	Homology	Domain
2.60.30.10	Mainly Beta	Sandwich	Electron Transport Ethylamine Dehydrogenase	Methylamine/Aralkylamine dehydrogenase light chain	2madL00

2AGLD 3PXTC 2BBKL 2I0RD 2AH0D 2I0SD 2OK6D 2J55L 2MTAL 4O1QC 4L3GC 2IUPD 4FA4C 4FA5C 4FA1C 2AH1D 3RLMC 2H3XB 2HKRD 4FAVC 3RN1C 2IAAB 4FB1C 1MDAL 4Y5RC 2HXCD 2OJYD 3L4OC 2Q7QD 3RN0C 2MADL 4FANC 2IUVD 2OIZD 2IURD 3PXSC 2I0TD 4K3IC 3RMZC 3PXWC 4L1QC 1MG3B 2IUQD 2HJBD 3SXTC 3SLEC 3C75L 3SWSC 1MAFL 2AGZD 2OK4D 3L4MC 3SVWC 1MG2B 2AGXD 1MAEL 4L3HC 2H47B 3SJLC 2J57K 2J56L 2HJ4D 3ORVC 2GC4B 2GC7B 2HKMD 4FA9C 2AGWD 2AGYD
chains in the Genus database with same CATH superfamily

#chains in the Genus database with same CATH superfamily
 2AGL D;  3PXT C;  2BBK L;  2I0R D;  2AH0 D;  2I0S D;  2OK6 D;  2J55 L;  2MTA L;  4O1Q C;  4L3G C;  2IUP D;  4FA4 C;  4FA5 C;  4FA1 C;  2AH1 D;  3RLM C;  2H3X B;  2HKR D;  4FAV C;  3RN1 C;  2IAA B;  4FB1 C;  1MDA L;  4Y5R C;  2HXC D;  2OJY D;  3L4O C;  2Q7Q D;  3RN0 C;  2MAD L;  4FAN C;  2IUV D;  2OIZ D;  2IUR D;  3PXS C;  2I0T D;  4K3I C;  3RMZ C;  3PXW C;  4L1Q C;  1MG3 B;  2IUQ D;  2HJB D;  3SXT C;  3SLE C;  3C75 L;  3SWS C;  1MAF L;  2AGZ D;  2OK4 D;  3L4M C;  3SVW C;  1MG2 B;  2AGX D;  1MAE L;  4L3H C;  2H47 B;  3SJL C;  2J57 K;  2J56 L;  2HJ4 D;  3ORV C;  2GC4 B;  2GC7 B;  2HKM D;  4FA9 C;  2AGW D;  2AGY D; 
#chains in the Genus database with same CATH topology
 2AGL D;  3PXT C;  2BBK L;  2I0R D;  2AH0 D;  2I0S D;  2OK6 D;  2J55 L;  2MTA L;  4O1Q C;  4L3G C;  2IUP D;  4FA4 C;  4FA5 C;  4FA1 C;  2AH1 D;  3RLM C;  2H3X B;  2HKR D;  4FAV C;  3RN1 C;  2IAA B;  4FB1 C;  1MDA L;  4Y5R C;  2HXC D;  2OJY D;  3L4O C;  2Q7Q D;  3RN0 C;  2MAD L;  4FAN C;  2IUV D;  2OIZ D;  2IUR D;  3PXS C;  2I0T D;  4K3I C;  3RMZ C;  3PXW C;  4L1Q C;  1MG3 B;  2IUQ D;  2HJB D;  3SXT C;  3SLE C;  3C75 L;  3SWS C;  1MAF L;  2AGZ D;  2OK4 D;  3L4M C;  3SVW C;  1MG2 B;  2AGX D;  1MAE L;  4L3H C;  2H47 B;  3SJL C;  2J57 K;  2J56 L;  2HJ4 D;  3ORV C;  2GC4 B;  2GC7 B;  2HKM D;  4FA9 C;  2AGW D;  2AGY D; 
#chains in the Genus database with same CATH homology
 2AGL D;  3PXT C;  2BBK L;  2I0R D;  2AH0 D;  2I0S D;  2OK6 D;  2J55 L;  2MTA L;  4O1Q C;  4L3G C;  2IUP D;  4FA4 C;  4FA5 C;  4FA1 C;  2AH1 D;  3RLM C;  2H3X B;  2HKR D;  4FAV C;  3RN1 C;  2IAA B;  4FB1 C;  1MDA L;  4Y5R C;  2HXC D;  2OJY D;  3L4O C;  2Q7Q D;  3RN0 C;  2MAD L;  4FAN C;  2IUV D;  2OIZ D;  2IUR D;  3PXS C;  2I0T D;  4K3I C;  3RMZ C;  3PXW C;  4L1Q C;  1MG3 B;  2IUQ D;  2HJB D;  3SXT C;  3SLE C;  3C75 L;  3SWS C;  1MAF L;  2AGZ D;  2OK4 D;  3L4M C;  3SVW C;  1MG2 B;  2AGX D;  1MAE L;  4L3H C;  2H47 B;  3SJL C;  2J57 K;  2J56 L;  2HJ4 D;  3ORV C;  2GC4 B;  2GC7 B;  2HKM D;  4FA9 C;  2AGW D;  2AGY D;

...loading similar chains, please wait...
similar chains in the Genus database (?% sequence similarity)

...loading similar chains, please wait...
similar chains in the pdb database (?% sequence similarity)

#similar chains in the Genus database (?% sequence similarity)
...loading similar chains, please wait...
#similar chains, but unknotted
...loading similar chains, please wait...
#similar chains in the pdb database (?% sequence similarity)
...loading similar chains, please wait...

2MADL

Total Genus

Knots found

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations